#6 Unable to find database file

[Dimitri Desvillechabrol]

Hello,

I am currently using scalpel to call INDEL and I'm using this command's line:

scalpel --verbose --single --bam file.bam --bed file.bed --ref file.fa --numprocs 8 --dir Single --logs

The software runs perfectly, but I was unable to find the database.db file. Indeed, I would need it to test other filtering criteria.

ls Single/
bamfile.bam header.txt logs readgroups.txt variants.db.dir variants.db.pag
bamfile.bam.bai loc2keys.txt.gz parameters.txt variants.5x.indel.vcf variants.db.lock

The file is present during the run but it is erase afterward.

Printing loc2key DB to file...
-- Exporting SVs to file
Command: ExportVariants.pl --db /pasteur/projets/specific/PFBAG_ngs/Projets/Philippe-G/Desvillechabrol/Scalpel_test/Single/variants.db --bed ../Colonies/ERR036017.bed --ref t126_n1_c8.fa --format vcf --type indel --mincov 5 --maxcov 1000000 --covratio 0.05 > /pasteur/projets/specific/PFBAG_ngs/Projets/Philippe-G/Desvillechabrol/Scalpel_test/Single/variants.5x.indel.vcf

Do you know why variants.db disappears and how can I retrieve it?

Thanks,
Dimitri

[Giuseppe Narzisi]

Hi Dimitri,

the database file should be available if the run completed without errors. At no point the database is deleted by the program. Have you tried re-running (possibly on a smaller input BAM) to check if you have the same problem? Can you please attach the full output? Thanks.

[Dimitri Desvillechabrol]

Hello Giuseppe,

I tried to use scalpel with a smaller .bed and .bam file but I had the same issue.
I attach the complete output to this message.

Thanks,
Dimitri

[Giuseppe Narzisi]

Based on the log file the program completed without errors. Not sure why you cannot find the DB file. I will need the small BAM, BED and REFERENCE files to reproduce the behavior myself. Thanks.

[Giuseppe Narzisi]

Actually the DB is present in the One_contig directory, is called:

"variants.db.dir"

in order to try other parameter settings for exporting mutations you simply need to provide "variants.db" (without any of the .dir .log. pag extensions) as input to the export module and it will work.

[Dimitri Desvillechabrol]

It works. Thank you very much.

Have a nice day,
Dimitri